Hindsight and all that good stuff, when you get runs or any other defects in the substrate (sealer, primer, whatever), stop there, fix the defects, and once corrected, then paint your topcoats. As you've seen, topcoats don't hide flaws.
Once you sanded through the top layer into the sealer, you have exposed the bond between the two layers. Then when you spray on top of this (with the urethane I take it?), you have solvents that attack and loosen this bond, hence the wrinkles. You'll need to resand, feather out the edges, and cover with sealer before proceeding any further. For spraying sealer over an exposed edge like that, I think you'll find a light coat on the initial application will help to seal it off without lifting again.
